Overview

Integrating multiple omics datasets allows researchers to gain a holistic view of biological systems. For example, combining ATAC-seq, RNA-seq, ChIP-seq, and Bisulfite-seq can reveal the interplay between chromatin accessibility, gene expression, histone modifications, and DNA methylation. This 2-day course focuses on the practical application of R for integrating and visualizing such multi-omics data. Participants will learn to process and combine these datasets, create overlap matrices to identify regions of co-occurrence, perform functional analysis of results, and master visualization techniques to communicate complex findings effectively. The course emphasizes hands-on exercises and a project-based approach, enabling participants to directly apply these skills to their own research questions.

Audience

This course is aimed at PhD students, postdoctoral and other researchers in the life sciences who are seeking to understand and visualize multi-omics data, aiming to integrate and interpret high-throughput biological data using R.

Learning outcomes

At the end of the course, the participants are expected to:

Import and integrate pre-processed ATAC-seq, RNA-seq, ChIP-seq, and Bisulfite-seq data using R and Bioconductor packages.
Generate and interpret overlap matrices to identify regions of co-occurrence and regulation.
Perform functional analysis of the results.
Create informative and visually appealing plots to represent multi-omics data.

Prerequisites

Knowledge / competencies

You should meet the learning outcomes of First Steps with R in Life Sciences.

This course is designed for beginners in multi-omics analysis, thus no requirement for prior experience in multi-omics analysis is needed. A basic understanding of R programming and fundamental biological concepts related to gene expression and epigenetics is highly recommended. Please evaluate your R skills here before registering.

Technical

Attendees should have a Wi-Fi enabled computer. An online R and RStudio-server environment will be provided.

In case you wish to perform the practical exercises on your own computer, please make sure that your laptop contain over 8GB of RAM, and please take a moment to install the following before the course:

R version > 4.2.
Latest RStudio version, the free version is perfectly fine.

Application

The registration fees for academics are CHF 200 and CHF 1000 for for-profit companies. While participants are registered on a first come, first served basis, exceptions may be made to ensure diversity and equity, which may increase the time before your registration is confirmed.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Applications close on 09/06/2025 or as soon as the places will be filled up. Deadline for free-of-charge cancellation is set to 09/06/2025. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

The course will take at the University of Zürich.

The course will start at 9:15 and end around 17:00.

Precise information will be provided to the participants in due time.

Additional information

Coordination: Geert van Geest

We will recommend 0.5 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.

Biology-informed Multiomics Data Integration and Visualization